Closed trvrb closed 10 years ago
I know there were previous comments on the terminology here being confusing. The most difficult piece is not having a single standard term to refer to each of the 4 groups of viruses we're dealing with: A/H3N2, A/H1N1, B/Vic and B/Yam. H3 and H1 are referred to as "subtypes" and Vic and Yam are referred to as "lineages". Lineage is already problematic because it can refer to a number of different phylogenetic scales; any single branch on the tree is a lineage. It would be good to be more up front about nomenclature early in the MS. How about going with the following:
That seems like a logical nomenclature proposal to me. With this in mind, I would recommend changes (in bold, did not intend to shout) along this line in the introduction paragraph to make this more explicit
Before 2009, there were four major influenza VARIANTS [to avoid the use of clades and lineages here] circulating within the human population: the H3N2 and H1N1 subtypes of influenza TYPE A, and the Victoria and Yamagata lineages of influenza TYPE B. In the case of influenza A, subtypes A/H3N2 and A/H1N1 refer to the genes, hemagglutinin (H or HA) and neuraminidase (N or NA), that are primarily responsible for the antigenic character of a strain. In the case of influenza B, THE TERM 'LINEAGE' IS USED [you could even add 'instead of subtypes] TO REFER TO Victoria (B/Vic) and Yamagata (B/Yam) AS antigenically distinct VARIANTS THAT diverged from a COMMON ANCESTOR prior to 1980 \cite{Rota90}.
And then remain consistent throughout the manuscript
I agree that this cleans up the paragraph, but I'm concerned about using variants here and then using lineages later. I'd like to chose something and stick with it. Possibilities include:
Thinking about this more now, I might be inclined to go with virus actually. John and Alan made some corrections to the text in this direction.
We've cleaned up our language regarding clades and lineages in the text. We consider A/H3N2, A/H1N1, B/Vic and B/Yam to each represent separate lineages of influenza. We no longer refer to separate clades.